There is a case where the names of indexed documents are changed on disk but the indexed group that points to those files in the file system has not (yet) been updated in a database. Or there is a case where the indexed documents are moved in the filesystem from one subfolder of an indexed folder to another.
In these cases Verify & Repair reports that the files are “missing”. They are not missing. The index merely hasn’t been updated.
I suggest causing V&R to first update all indexed items before examining records for “missing”.
(Someone will suggest moving things into the data base, fiddling with names and folders there and then moving them back external – that is NOT an answer. IMO the V&R logic is what’s broken.)